LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-583-g5868aa095d-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
  using 1 OpenMP thread(s) per MPI task
# two monomer nylon example
# reaction produces a condensed water molecule

units real

boundary p p p

atom_style full

kspace_style pppm 1.0e-4

pair_style lj/class2/coul/long 8.5

angle_style class2

bond_style class2

dihedral_style class2

improper_style class2

special_bonds lj/coul 0 0 1
pair_modify tail yes mix sixthpower

read_data tiny_nylon.data   extra/bond/per/atom 5    extra/angle/per/atom 15   extra/dihedral/per/atom 15   extra/improper/per/atom 25   extra/special/per/atom 25
Reading data file ...
  orthogonal box = (-25 -25 -25) to (25 25 25)
  1 by 2 by 2 MPI processor grid
  reading atom labelmap ...
  reading bond labelmap ...
  reading angle labelmap ...
  reading dihedral labelmap ...
  reading improper labelmap ...
  reading atoms ...
  44 atoms
  reading velocities ...
  44 velocities
  scanning bonds ...
  9 = max bonds/atom
  scanning angles ...
  21 = max angles/atom
  scanning dihedrals ...
  29 = max dihedrals/atom
  scanning impropers ...
  29 = max impropers/atom
  orthogonal box = (-25 -25 -25) to (25 25 25)
  1 by 2 by 2 MPI processor grid
  reading bonds ...
  42 bonds
  reading angles ...
  74 angles
  reading dihedrals ...
  100 dihedrals
  reading impropers ...
  16 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        1       
  special bond factors coul:  0        0        1       
     4 = max # of 1-2 neighbors
     6 = max # of 1-3 neighbors
    35 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.006 seconds

velocity all create 300.0 4928459 dist gaussian

molecule mol1 rxn1_stp1_unreacted.json
Read molecule template mol1:
(no title)
  1 molecules
  0 fragments
  18 atoms with max type 0
  16 bonds with max type 8
  25 angles with max type 25
  23 dihedrals with max type 33
  2 impropers with max type 3
molecule mol2 rxn1_stp1_reacted.json
Read molecule template mol2:
(no title)
  1 molecules
  0 fragments
  18 atoms with max type 0
  17 bonds with max type 11
  31 angles with max type 24
  39 dihedrals with max type 30
  0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.json
Read molecule template mol3:
(no title)
  1 molecules
  0 fragments
  15 atoms with max type 0
  14 bonds with max type 11
  25 angles with max type 24
  30 dihedrals with max type 30
  0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.json
Read molecule template mol4:
(no title)
  1 molecules
  0 fragments
  15 atoms with max type 0
  13 bonds with max type 13
  19 angles with max type 26
  16 dihedrals with max type 29
  2 impropers with max type 5

thermo 50

# dump 1 all xyz 1 test_vis.xyz
# dump_modify 1 types labels

fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes
WARNING: Fix bond/react: Atom affected by reaction rxn1 is too close to template edge (src/REACTION/fix_bond_react.cpp:2708)
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (src/REACTION/fix_bond_react.cpp:2708)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined

fix 1 statted_grp_REACT nvt temp 300 300 100

# optionally, you can customize behavior of reacting atoms,
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1

thermo_style custom step temp press density f_myrxns[*]

# restart 100 restart1 restart2

run 10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419

@Article{Gissinger24,
 author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
 title = {Type Label Framework for Bonded Force Fields in LAMMPS},
 journal = {J. Phys. Chem. B},
 year =    2024,
 volume =  128,
 number =  13,
 pages =   {3282--3297}
}

- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012, doi:10.1016/j.cpc.2024.109287

@Article{Gissinger17,
 author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
 title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
 journal = {Polymer},
 year =    2017,
 volume =  128,
 pages =   {211--217}
}

@Article{Gissinger20,
 author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
 title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
 journal = {Macromolecules},
 year =    2020,
 volume =  53,
 number =  22,
 pages =   {9953--9961}
}

@Article{Gissinger24,
 author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
 title = {Molecular Modeling of Reactive Systems with REACTER},
 journal = {Computer Physics Communications},
 year =    2024,
 volume =  304,
 number =  109287
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
  G vector (1/distance) = 0.23408048
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.018627396
  estimated relative force accuracy = 5.6095851e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 3380 960
Generated 55 of 55 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10.5
  ghost atom cutoff = 10.5
  binsize = 5.25, bins = 10 10 10
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) pair lj/class2/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (2) fix bond/react, occasional, copy from (1)
      attributes: half, newton on
      pair build: copy
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 33.49 | 33.72 | 34.28 Mbytes
   Step          Temp          Press         Density      f_myrxns[1]    f_myrxns[2]  
         0   300            357.25588      0.0034851739   0              0            
        50   328.952       -39.291672      0.0034851739   1              0            
       100   311.59495      29.741131      0.0034851739   1              1            
       150   325.04965     -19.624049      0.0034851739   1              1            
       200   313.15254      15.730975      0.0034851739   1              1            
       250   307.88805     -22.944869      0.0034851739   1              1            
       300   287.9343       6.7916738      0.0034851739   1              1            
       350   314.40601      12.913246      0.0034851739   1              1            
       400   304.58587      6.9804459      0.0034851739   1              1            
       450   300.97668      14.68689       0.0034851739   1              1            
       500   345.19498     -29.961085      0.0034851739   1              1            
       550   229.37329      12.88087       0.0034851739   1              1            
       600   239.75504     -3.575567       0.0034851739   1              1            
       650   257.58951     -5.0844118      0.0034851739   1              1            
       700   249.84121      22.825491      0.0034851739   1              1            
       750   287.62022      28.059197      0.0034851739   1              1            
       800   352.31339     -50.233738      0.0034851739   1              1            
       850   316.12821      22.493396      0.0034851739   1              1            
       900   283.85252      26.129698      0.0034851739   1              1            
       950   290.30591     -25.743121      0.0034851739   1              1            
      1000   346.57856     -2.1188627      0.0034851739   1              1            
      1050   251.23391      20.636107      0.0034851739   1              1            
      1100   267.48303     -15.912571      0.0034851739   1              1            
      1150   282.66256      14.019753      0.0034851739   1              1            
      1200   227.56518     -27.076623      0.0034851739   1              1            
      1250   232.7204      -1.0387593      0.0034851739   1              1            
      1300   277.28783      32.449571      0.0034851739   1              1            
      1350   308.5732      -11.129035      0.0034851739   1              1            
      1400   264.96641     -20.93416       0.0034851739   1              1            
      1450   262.83931      30.82366       0.0034851739   1              1            
      1500   276.23182     -24.480049      0.0034851739   1              1            
      1550   319.00599     -9.8372065      0.0034851739   1              1            
      1600   316.48228     -15.940319      0.0034851739   1              1            
      1650   277.213        1.3856424      0.0034851739   1              1            
      1700   302.34736     -27.623644      0.0034851739   1              1            
      1750   312.06738     -52.786773      0.0034851739   1              1            
      1800   232.82457     -8.2208725      0.0034851739   1              1            
      1850   219.66312      0.0019675712   0.0034851739   1              1            
      1900   245.49515     -24.2089        0.0034851739   1              1            
      1950   262.40648     -1.8634053      0.0034851739   1              1            
      2000   307.5184       10.588572      0.0034851739   1              1            
      2050   316.54878      8.3925573      0.0034851739   1              1            
      2100   318.99324      29.042199      0.0034851739   1              1            
      2150   352.69886      18.443891      0.0034851739   1              1            
      2200   326.32556     -38.670827      0.0034851739   1              1            
      2250   333.73083      15.388091      0.0034851739   1              1            
      2300   258.51644     -42.524579      0.0034851739   1              1            
      2350   259.55019     -23.484534      0.0034851739   1              1            
      2400   289.75114      28.367991      0.0034851739   1              1            
      2450   312.34376      10.34566       0.0034851739   1              1            
      2500   298.65847     -14.077574      0.0034851739   1              1            
      2550   237.48617     -55.545492      0.0034851739   1              1            
      2600   266.79719     -17.165888      0.0034851739   1              1            
      2650   297.32793     -30.336065      0.0034851739   1              1            
      2700   258.77594     -1.3622773      0.0034851739   1              1            
      2750   240.05564     -0.44186476     0.0034851739   1              1            
      2800   189.88736     -13.20747       0.0034851739   1              1            
      2850   260.84014     -18.597268      0.0034851739   1              1            
      2900   299.99469     -7.3249657      0.0034851739   1              1            
      2950   377.90515      18.041562      0.0034851739   1              1            
      3000   263.92164     -54.260872      0.0034851739   1              1            
      3050   273.63965      26.974167      0.0034851739   1              1            
      3100   276.52188     -3.8587984      0.0034851739   1              1            
      3150   351.27821      84.898762      0.0034851739   1              1            
      3200   327.48898     -10.338223      0.0034851739   1              1            
      3250   356.1212       16.719521      0.0034851739   1              1            
      3300   263.02135     -18.034405      0.0034851739   1              1            
      3350   285.4132      -24.466598      0.0034851739   1              1            
      3400   233.65385     -39.293822      0.0034851739   1              1            
      3450   276.32817      44.300742      0.0034851739   1              1            
      3500   300.43096      28.490491      0.0034851739   1              1            
      3550   254.03694     -24.336803      0.0034851739   1              1            
      3600   304.68561      4.5774591      0.0034851739   1              1            
      3650   321.19694     -15.472971      0.0034851739   1              1            
      3700   256.01801      25.355422      0.0034851739   1              1            
      3750   356.6048      -5.4033701      0.0034851739   1              1            
      3800   361.31685     -1.4920086      0.0034851739   1              1            
      3850   253.81335     -1.20491        0.0034851739   1              1            
      3900   257.99176      19.272863      0.0034851739   1              1            
      3950   261.56599     -47.578625      0.0034851739   1              1            
      4000   254.55501     -8.6462427      0.0034851739   1              1            
      4050   301.57465      22.466646      0.0034851739   1              1            
      4100   304.71812     -31.337506      0.0034851739   1              1            
      4150   307.05688      0.54710967     0.0034851739   1              1            
      4200   291.11678      51.789059      0.0034851739   1              1            
      4250   333.71702     -24.64525       0.0034851739   1              1            
      4300   370.53725     -11.852814      0.0034851739   1              1            
      4350   407.98596      8.5128018      0.0034851739   1              1            
      4400   329.43106     -25.637208      0.0034851739   1              1            
      4450   366.91557      26.250029      0.0034851739   1              1            
      4500   311.63134      31.61568       0.0034851739   1              1            
      4550   292.18008      13.020734      0.0034851739   1              1            
      4600   320.76549     -49.324846      0.0034851739   1              1            
      4650   271.72115     -3.6666938      0.0034851739   1              1            
      4700   305.52974      38.114013      0.0034851739   1              1            
      4750   304.37057      52.050863      0.0034851739   1              1            
      4800   300.50548      13.158616      0.0034851739   1              1            
      4850   317.66606     -14.951608      0.0034851739   1              1            
      4900   331.39591      23.823575      0.0034851739   1              1            
      4950   340.899       -19.557136      0.0034851739   1              1            
      5000   414.45112      8.7124515      0.0034851739   1              1            
      5050   382.95479      18.555744      0.0034851739   1              1            
      5100   381.26344      22.674486      0.0034851739   1              1            
      5150   309.88477      36.184971      0.0034851739   1              1            
      5200   312.4976      -31.403643      0.0034851739   1              1            
      5250   285.1896      -36.180241      0.0034851739   1              1            
      5300   249.68604     -55.078779      0.0034851739   1              1            
      5350   251.76542      12.156887      0.0034851739   1              1            
      5400   278.40908      15.846527      0.0034851739   1              1            
      5450   281.22116     -12.005198      0.0034851739   1              1            
      5500   362.38064     -14.608206      0.0034851739   1              1            
      5550   287.39255      38.446058      0.0034851739   1              1            
      5600   264.87699     -20.21112       0.0034851739   1              1            
      5650   300.31424     -15.899086      0.0034851739   1              1            
      5700   318.6444       18.688317      0.0034851739   1              1            
      5750   321.74224     -7.5355749      0.0034851739   1              1            
      5800   314.65871      33.512178      0.0034851739   1              1            
      5850   307.11597     -16.492491      0.0034851739   1              1            
      5900   259.10441     -49.668159      0.0034851739   1              1            
      5950   292.09045     -22.04962       0.0034851739   1              1            
      6000   243.99229     -15.110485      0.0034851739   1              1            
      6050   276.66494     -21.052012      0.0034851739   1              1            
      6100   328.39444      64.522811      0.0034851739   1              1            
      6150   289.49991     -18.518616      0.0034851739   1              1            
      6200   358.50076     -9.3115021      0.0034851739   1              1            
      6250   303.15143     -42.618735      0.0034851739   1              1            
      6300   297.17364      18.116143      0.0034851739   1              1            
      6350   254.2382       2.4963759      0.0034851739   1              1            
      6400   227.56255      23.535315      0.0034851739   1              1            
      6450   280.70805      13.243012      0.0034851739   1              1            
      6500   251.14485     -18.466759      0.0034851739   1              1            
      6550   284.32321      9.0351234      0.0034851739   1              1            
      6600   284.03779     -10.683306      0.0034851739   1              1            
      6650   315.1569      -39.736019      0.0034851739   1              1            
      6700   302.50424      5.9013011      0.0034851739   1              1            
      6750   368.279        44.343503      0.0034851739   1              1            
      6800   279.67266     -35.967233      0.0034851739   1              1            
      6850   298.98045      3.0539699      0.0034851739   1              1            
      6900   236.94852      0.55971293     0.0034851739   1              1            
      6950   303.38382     -9.1880246      0.0034851739   1              1            
      7000   264.56096      3.904024       0.0034851739   1              1            
      7050   272.26968     -44.608801      0.0034851739   1              1            
      7100   235.38132      13.141913      0.0034851739   1              1            
      7150   272.0985       26.601686      0.0034851739   1              1            
      7200   314.41177     -7.6236617      0.0034851739   1              1            
      7250   313.29915     -45.214663      0.0034851739   1              1            
      7300   309.20548     -11.691744      0.0034851739   1              1            
      7350   342.22769      18.805899      0.0034851739   1              1            
      7400   301.02701      32.830071      0.0034851739   1              1            
      7450   318.19524      48.620851      0.0034851739   1              1            
      7500   290.00663     -9.1444424      0.0034851739   1              1            
      7550   238.07666      32.654941      0.0034851739   1              1            
      7600   275.95317     -23.982336      0.0034851739   1              1            
      7650   274.54472     -29.183684      0.0034851739   1              1            
      7700   307.25317      11.981268      0.0034851739   1              1            
      7750   299.40271     -19.390542      0.0034851739   1              1            
      7800   314.18813     -6.0794802      0.0034851739   1              1            
      7850   271.14043      40.491364      0.0034851739   1              1            
      7900   266.43792      37.250574      0.0034851739   1              1            
      7950   330.21996      31.783381      0.0034851739   1              1            
      8000   313.80294      44.878972      0.0034851739   1              1            
      8050   331.1094       1.9597746      0.0034851739   1              1            
      8100   267.80448      26.159121      0.0034851739   1              1            
      8150   267.17305      16.135234      0.0034851739   1              1            
      8200   290.248       -13.058622      0.0034851739   1              1            
      8250   231.77635     -42.850795      0.0034851739   1              1            
      8300   233.58288      29.137765      0.0034851739   1              1            
      8350   270.2913      -11.177011      0.0034851739   1              1            
      8400   254.69873      3.1775639      0.0034851739   1              1            
      8450   334.88277     -27.336924      0.0034851739   1              1            
      8500   354.95137     -9.751911       0.0034851739   1              1            
      8550   327.78998      8.2348621      0.0034851739   1              1            
      8600   306.15772      1.3756734      0.0034851739   1              1            
      8650   325.68699      6.5939205      0.0034851739   1              1            
      8700   302.84804      13.912169      0.0034851739   1              1            
      8750   299.34988      10.311212      0.0034851739   1              1            
      8800   258.77684     -8.0783535      0.0034851739   1              1            
      8850   299.8835      -9.61362        0.0034851739   1              1            
      8900   350.28205     -34.897861      0.0034851739   1              1            
      8950   316.90133     -52.845562      0.0034851739   1              1            
      9000   337.50548      18.172556      0.0034851739   1              1            
      9050   306.67254      37.062973      0.0034851739   1              1            
      9100   310.74844      58.178538      0.0034851739   1              1            
      9150   301.53463      5.9650738      0.0034851739   1              1            
      9200   284.61384      10.677528      0.0034851739   1              1            
      9250   247.86475     -15.325203      0.0034851739   1              1            
      9300   309.74481     -60.070902      0.0034851739   1              1            
      9350   290.17111      5.6049467      0.0034851739   1              1            
      9400   268.79925     -9.2423032      0.0034851739   1              1            
      9450   315.80445      18.124612      0.0034851739   1              1            
      9500   351.58161     -14.465115      0.0034851739   1              1            
      9550   344.93028      43.161438      0.0034851739   1              1            
      9600   265.92273      0.3396608      0.0034851739   1              1            
      9650   261.1649      -20.46043       0.0034851739   1              1            
      9700   262.05627      27.187613      0.0034851739   1              1            
      9750   249.12463      15.911339      0.0034851739   1              1            
      9800   262.40626     -16.159153      0.0034851739   1              1            
      9850   267.48677      0.32143902     0.0034851739   1              1            
      9900   316.15674      40.664589      0.0034851739   1              1            
      9950   323.94181      20.356291      0.0034851739   1              1            
     10000   307.90841      4.8392456      0.0034851739   1              1            
Loop time of 0.937214 on 4 procs for 10000 steps with 44 atoms

Performance: 921.881 ns/day, 0.026 hours/ns, 10669.916 timesteps/s, 469.476 katom-step/s
96.5% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.00042896 | 0.01827    | 0.04944    |  14.9 |  1.95
Bond    | 0.00067626 | 0.061292   | 0.18867    |  31.0 |  6.54
Kspace  | 0.50738    | 0.64527    | 0.7136     |  10.4 | 68.85
Neigh   | 0.0031476  | 0.0031815  | 0.0032165  |   0.0 |  0.34
Comm    | 0.01335    | 0.020817   | 0.035424   |   6.1 |  2.22
Output  | 0.0010449  | 0.0012202  | 0.0016969  |   0.8 |  0.13
Modify  | 0.16314    | 0.18266    | 0.20201    |   4.3 | 19.49
Other   |            | 0.004499   |            |       |  0.48

Nlocal:             11 ave          40 max           0 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Nghost:             22 ave          40 max           4 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs:          216.5 ave         845 max           0 min
Histogram: 3 0 0 0 0 0 0 0 0 1

Total # of neighbors = 866
Ave neighs/atom = 19.681818
Ave special neighs/atom = 6.4090909
Neighbor list builds = 212
Dangerous builds = 0

# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:00
